"""
    Memory Management Module

Advanced memory management and optimization utilities for GSICoreAnalysis.jl including:
- Memory pooling for frequent allocations
- Efficient data copying and transformation
- Memory usage monitoring and automatic GC triggers
- Buffer management for I/O operations
- Memory-mapped file access for large datasets
- Reference counting and object lifecycle management

# Usage

```julia
using GSICoreAnalysis.Performance.MemoryManagement

# Create memory pool for observations
obs_pool = MemoryPool{ObservationType}(initial_size=1000, max_size=10000)

# Allocate from pool
obs = allocate_from_pool(obs_pool, observation_data)

# Automatic memory monitoring
memory_monitor = MemoryMonitor(
    gc_threshold = 0.8,
    monitoring_interval = 10,
    enable_alerts = true
)

start_memory_monitoring(memory_monitor)

# Memory-mapped file access
mmap_reader = MemoryMappedReader("large_dataset.dat")
data_chunk = read_chunk(mmap_reader, offset, size)

# Buffer management for I/O
io_buffer = IOBufferManager(buffer_size=1024*1024)  # 1MB buffer
buffered_data = read_with_buffer(io_buffer, data_source)
```
"""
module MemoryManagement

using Mmap
using Printf
using Dates
using Base.Threads
using Statistics
using LinearAlgebra

# Export main types and functions
export MemoryPool, MemoryMonitor, IOBufferManager
export MemoryMappedReader, MemoryMappedWriter
export EfficientDataTransform, ReferenceCounter
export allocate_from_pool, return_to_pool, reset_pool
export start_memory_monitoring, stop_memory_monitoring
export create_memory_mapped_reader, create_memory_mapped_writer
export efficient_copy, efficient_transform, in_place_transform
export track_memory_usage, get_memory_stats, trigger_gc_if_needed
export optimize_memory_layout, minimize_allocations
export buffer_io_operations, manage_temporary_data

"""
    MemoryPool{T}

Memory pool for efficient allocation and reuse of objects of type T.
"""
mutable struct MemoryPool{T}
    available_objects::Vector{T}
    allocated_objects::Set{UInt64}
    max_size::Int
    current_size::Int
    hit_count::Int
    miss_count::Int
    creation_function::Union{Nothing, Function}
    reset_function::Union{Nothing, Function}
    
    function MemoryPool{T}(;
        initial_size::Int = 100,
        max_size::Int = 1000,
        creation_function::Union{Nothing, Function} = nothing,
        reset_function::Union{Nothing, Function} = nothing
    ) where T
        available_objects = Vector{T}()
        allocated_objects = Set{UInt64}()
        
        # Pre-allocate initial objects if creation function provided
        if creation_function !== nothing
            for _ in 1:initial_size
                push!(available_objects, creation_function())
            end
        end
        
        new{T}(available_objects, allocated_objects, max_size, 
               length(available_objects), 0, 0, creation_function, reset_function)
    end
end

"""
    MemoryMonitor

Monitors memory usage and triggers garbage collection when needed.
"""
mutable struct MemoryMonitor
    gc_threshold::Float64
    monitoring_interval::Int  # seconds
    enable_alerts::Bool
    is_monitoring::Bool
    monitor_task::Union{Nothing, Task}
    memory_history::Vector{Float64}
    max_history_size::Int
    alert_callback::Union{Nothing, Function}
    
    function MemoryMonitor(;
        gc_threshold::Float64 = 0.8,
        monitoring_interval::Int = 10,
        enable_alerts::Bool = true,
        max_history_size::Int = 100,
        alert_callback::Union{Nothing, Function} = nothing
    )
        memory_history = Float64[]
        
        new(gc_threshold, monitoring_interval, enable_alerts, false,
            nothing, memory_history, max_history_size, alert_callback)
    end
end

"""
    IOBufferManager

Manages I/O buffers for efficient reading and writing.
"""
mutable struct IOBufferManager
    buffer_size::Int
    read_buffer::Vector{UInt8}
    write_buffer::Vector{UInt8}
    buffer_pools::Dict{Int, Vector{Vector{UInt8}}}
    active_buffers::Set{UInt64}
    
    function IOBufferManager(buffer_size::Int = 1024 * 1024)  # Default 1MB
        read_buffer = Vector{UInt8}(undef, buffer_size)
        write_buffer = Vector{UInt8}(undef, buffer_size)
        buffer_pools = Dict{Int, Vector{Vector{UInt8}}}()
        active_buffers = Set{UInt64}()
        
        new(buffer_size, read_buffer, write_buffer, buffer_pools, active_buffers)
    end
end

"""
    MemoryMappedReader

Efficient reader for large files using memory mapping.
"""
mutable struct MemoryMappedReader
    filepath::String
    file_handle::IOStream
    mmap_array::Vector{UInt8}
    file_size::Int64
    current_position::Int64
    
    function MemoryMappedReader(filepath::String)
        if !isfile(filepath)
            throw(ArgumentError("File does not exist: $filepath"))
        end
        
        file_handle = open(filepath, "r")
        file_size = filesize(filepath)
        mmap_array = Mmap.mmap(file_handle, Vector{UInt8}, (file_size,))
        
        new(filepath, file_handle, mmap_array, file_size, 1)
    end
end

"""
    MemoryMappedWriter

Efficient writer for large files using memory mapping.
"""
mutable struct MemoryMappedWriter
    filepath::String
    file_handle::IOStream
    mmap_array::Vector{UInt8}
    file_size::Int64
    current_position::Int64
    
    function MemoryMappedWriter(filepath::String, size::Int64)
        file_handle = open(filepath, "w+")
        
        # Pre-allocate file
        write(file_handle, zeros(UInt8, size))
        flush(file_handle)
        
        mmap_array = Mmap.mmap(file_handle, Vector{UInt8}, (size,))
        
        new(filepath, file_handle, mmap_array, size, 1)
    end
end

"""
    EfficientDataTransform

Container for efficient data transformation operations.
"""
struct EfficientDataTransform
    use_views::Bool
    minimize_copies::Bool
    in_place_operations::Bool
    
    EfficientDataTransform(;
        use_views = true,
        minimize_copies = true,
        in_place_operations = false
    ) = new(use_views, minimize_copies, in_place_operations)
end

"""
    ReferenceCounter

Reference counting system for managing object lifecycles.
"""
mutable struct ReferenceCounter{T}
    objects::Dict{UInt64, T}
    ref_counts::Dict{UInt64, Int}
    cleanup_function::Union{Nothing, Function}
    
    function ReferenceCounter{T}(cleanup_function::Union{Nothing, Function} = nothing) where T
        new{T}(Dict{UInt64, T}(), Dict{UInt64, Int}(), cleanup_function)
    end
end

# Global memory monitor instance
const GLOBAL_MEMORY_MONITOR = Ref{Union{Nothing, MemoryMonitor}}(nothing)

"""
    allocate_from_pool(pool::MemoryPool{T}) where T

Allocate an object from the memory pool.
"""
function allocate_from_pool(pool::MemoryPool{T}) where T
    if !isempty(pool.available_objects)
        # Reuse existing object
        obj = pop!(pool.available_objects)
        obj_id = objectid(obj)
        push!(pool.allocated_objects, obj_id)
        pool.hit_count += 1
        
        # Reset object if reset function provided
        if pool.reset_function !== nothing
            pool.reset_function(obj)
        end
        
        return obj
    else
        # Create new object if under limit
        if pool.current_size < pool.max_size && pool.creation_function !== nothing
            obj = pool.creation_function()
            obj_id = objectid(obj)
            push!(pool.allocated_objects, obj_id)
            pool.current_size += 1
            pool.miss_count += 1
            return obj
        else
            pool.miss_count += 1
            throw(OutOfMemoryError("Memory pool exhausted and cannot create new objects"))
        end
    end
end

"""
    allocate_from_pool(pool::MemoryPool{T}, init_data) where T

Allocate and initialize an object from the memory pool.
"""
function allocate_from_pool(pool::MemoryPool{T}, init_data) where T
    obj = allocate_from_pool(pool)
    
    # Initialize with provided data
    if hasmethod(initialize_object!, (T, typeof(init_data)))
        initialize_object!(obj, init_data)
    end
    
    return obj
end

"""
    return_to_pool(pool::MemoryPool{T}, obj::T) where T

Return an object to the memory pool for reuse.
"""
function return_to_pool(pool::MemoryPool{T}, obj::T) where T
    obj_id = objectid(obj)
    
    if obj_id in pool.allocated_objects
        delete!(pool.allocated_objects, obj_id)
        push!(pool.available_objects, obj)
        
        @debug "Object returned to pool" pool_type=T available=length(pool.available_objects)
    else
        @warn "Attempting to return object not allocated from this pool"
    end
end

"""
    reset_pool(pool::MemoryPool{T}) where T

Reset memory pool, clearing all objects.
"""
function reset_pool(pool::MemoryPool{T}) where T
    empty!(pool.available_objects)
    empty!(pool.allocated_objects)
    pool.current_size = 0
    pool.hit_count = 0
    pool.miss_count = 0
    
    @info "Memory pool reset" type=T
end

"""
    start_memory_monitoring(monitor::MemoryMonitor)

Start continuous memory monitoring.
"""
function start_memory_monitoring(monitor::MemoryMonitor)
    if monitor.is_monitoring
        @warn "Memory monitoring already active"
        return
    end
    
    monitor.is_monitoring = true
    GLOBAL_MEMORY_MONITOR[] = monitor
    
    monitor.monitor_task = @async begin
        while monitor.is_monitoring
            try
                memory_usage = get_memory_usage_fraction()
                push!(monitor.memory_history, memory_usage)
                
                # Limit history size
                if length(monitor.memory_history) > monitor.max_history_size
                    deleteat!(monitor.memory_history, 1)
                end
                
                # Check if GC needed
                if memory_usage > monitor.gc_threshold
                    @info "Memory usage high, triggering GC" usage=memory_usage threshold=monitor.gc_threshold
                    GC.gc()
                    
                    if monitor.enable_alerts && monitor.alert_callback !== nothing
                        monitor.alert_callback(memory_usage, monitor.gc_threshold)
                    end
                end
                
                sleep(monitor.monitoring_interval)
            catch e
                @error "Memory monitoring error" exception=e
                break
            end
        end
    end
    
    @info "Memory monitoring started" threshold=monitor.gc_threshold interval=monitor.monitoring_interval
end

"""
    stop_memory_monitoring(monitor::MemoryMonitor)

Stop memory monitoring.
"""
function stop_memory_monitoring(monitor::MemoryMonitor)
    monitor.is_monitoring = false
    
    if monitor.monitor_task !== nothing
        # Give the task time to finish
        sleep(0.1)
    end
    
    GLOBAL_MEMORY_MONITOR[] = nothing
    @info "Memory monitoring stopped"
end

"""
    get_memory_usage_fraction()

Get current memory usage as fraction of total system memory.
"""
function get_memory_usage_fraction()
    gc_stats = Base.gc_num()
    total_memory = Sys.total_memory()
    
    # Estimate current memory usage
    # This is approximate since Julia doesn't provide direct current usage
    free_memory = Sys.free_memory()
    used_memory = total_memory - free_memory
    
    return used_memory / total_memory
end

"""
    create_memory_mapped_reader(filepath::String)

Create memory-mapped reader for efficient large file access.
"""
function create_memory_mapped_reader(filepath::String)
    return MemoryMappedReader(filepath)
end

"""
    read_chunk(reader::MemoryMappedReader, offset::Int64, size::Int)

Read a chunk of data from memory-mapped file.
"""
function read_chunk(reader::MemoryMappedReader, offset::Int64, size::Int)
    if offset + size > reader.file_size
        throw(BoundsError("Read request exceeds file size"))
    end
    
    # Return view into memory-mapped array
    chunk_end = offset + size - 1
    return view(reader.mmap_array, offset:chunk_end)
end

"""
    create_memory_mapped_writer(filepath::String, size::Int64)

Create memory-mapped writer for efficient large file writing.
"""
function create_memory_mapped_writer(filepath::String, size::Int64)
    return MemoryMappedWriter(filepath, size)
end

"""
    write_chunk(writer::MemoryMappedWriter, data::AbstractVector{UInt8}, offset::Int64)

Write data chunk to memory-mapped file.
"""
function write_chunk(writer::MemoryMappedWriter, data::AbstractVector{UInt8}, offset::Int64)
    if offset + length(data) > writer.file_size
        throw(BoundsError("Write request exceeds file size"))
    end
    
    # Copy data into memory-mapped array
    chunk_end = offset + length(data) - 1
    writer.mmap_array[offset:chunk_end] .= data
    
    # Update position
    writer.current_position = offset + length(data)
end

"""
    efficient_copy(src::AbstractArray{T}, transform::EfficientDataTransform) where T

Create efficient copy of array data.
"""
function efficient_copy(src::AbstractArray{T}, transform::EfficientDataTransform) where T
    if transform.use_views && !transform.minimize_copies
        return view(src, :)
    elseif transform.minimize_copies
        # Return original if safe to do so
        return src
    else
        # Create explicit copy
        return copy(src)
    end
end

"""
    efficient_transform(src::AbstractArray{T}, func::Function,
                       transform::EfficientDataTransform) where T

Apply transformation function efficiently.
"""
function efficient_transform(src::AbstractArray{T}, func::Function,
                             transform::EfficientDataTransform) where T
    if transform.in_place_operations && applicable(func, src, src)
        # In-place transformation
        func(src, src)
        return src
    else
        # Create transformed copy
        return func(src)
    end
end

"""
    in_place_transform(data::AbstractArray{T}, func::Function) where T

Apply in-place transformation to minimize memory allocation.
"""
function in_place_transform(data::AbstractArray{T}, func::Function) where T
    @inbounds for i in eachindex(data)
        data[i] = func(data[i])
    end
    return data
end

"""
    track_memory_usage(operation_name::String, func::Function, args...)

Track memory usage of an operation.
"""
function track_memory_usage(operation_name::String, func::Function, args...)
    # Get initial memory stats
    initial_stats = Base.gc_num()
    initial_time = time()
    
    # Execute function
    result = func(args...)
    
    # Get final memory stats
    final_stats = Base.gc_num()
    final_time = time()
    
    # Calculate memory metrics
    allocated = final_stats.allocd - initial_stats.allocd
    freed = final_stats.freed - initial_stats.freed
    gc_time = final_stats.total_time - initial_stats.total_time
    execution_time = final_time - initial_time
    
    memory_stats = (
        operation = operation_name,
        allocated_bytes = allocated,
        freed_bytes = freed,
        net_allocated = allocated - freed,
        gc_time_ms = gc_time,
        execution_time_s = execution_time,
        gc_collections = final_stats.pause - initial_stats.pause
    )
    
    @info "Memory usage tracked" memory_stats...
    
    return result, memory_stats
end

"""
    get_memory_stats()

Get current memory statistics.
"""
function get_memory_stats()
    gc_stats = Base.gc_num()
    
    return (
        total_allocated = gc_stats.allocd,
        total_freed = gc_stats.freed,
        current_live = gc_stats.allocd - gc_stats.freed,
        gc_collections = gc_stats.pause,
        gc_time_ms = gc_stats.total_time,
        system_total_gb = Sys.total_memory() / (1024^3),
        system_free_gb = Sys.free_memory() / (1024^3)
    )
end

"""
    trigger_gc_if_needed(threshold::Float64 = 0.8)

Trigger garbage collection if memory usage exceeds threshold.
"""
function trigger_gc_if_needed(threshold::Float64 = 0.8)
    memory_fraction = get_memory_usage_fraction()
    
    if memory_fraction > threshold
        @info "Triggering GC due to high memory usage" usage=memory_fraction threshold=threshold
        GC.gc()
        
        # Get updated memory usage
        new_memory_fraction = get_memory_usage_fraction()
        memory_freed = memory_fraction - new_memory_fraction
        
        @info "GC completed" old_usage=memory_fraction new_usage=new_memory_fraction freed=memory_freed
        
        return true
    end
    
    return false
end

"""
    optimize_memory_layout(data::Vector{T}) where T

Optimize memory layout of data for better cache performance.
"""
function optimize_memory_layout(data::Vector{T}) where T
    # For simple types, ensure contiguous memory
    if isbitstype(T)
        # Data is already optimally laid out for bits types
        return data
    end
    
    # For complex types, consider structure-of-arrays transformation
    @info "Memory layout optimization" type=T size=length(data) is_bits_type=isbitstype(T)
    
    # Placeholder for more complex optimization
    return data
end

"""
    minimize_allocations(func::Function, args...)

Execute function while minimizing allocations.
"""
function minimize_allocations(func::Function, args...)
    # Disable GC temporarily to prevent interruptions
    was_enabled = GC.enable(false)
    
    try
        result = func(args...)
        return result
    finally
        # Re-enable GC
        GC.enable(was_enabled)
        
        # Trigger GC now if it was previously enabled
        if was_enabled
            GC.gc()
        end
    end
end

"""
    get_buffer(buffer_manager::IOBufferManager, size::Int)

Get I/O buffer of specified size from buffer manager.
"""
function get_buffer(buffer_manager::IOBufferManager, size::Int)
    if size <= buffer_manager.buffer_size
        # Use pre-allocated buffer
        return view(buffer_manager.read_buffer, 1:size)
    else
        # Check if we have a pooled buffer of this size
        if haskey(buffer_manager.buffer_pools, size)
            pool = buffer_manager.buffer_pools[size]
            if !isempty(pool)
                buffer = pop!(pool)
                buffer_id = objectid(buffer)
                push!(buffer_manager.active_buffers, buffer_id)
                return buffer
            end
        end
        
        # Create new buffer
        buffer = Vector{UInt8}(undef, size)
        buffer_id = objectid(buffer)
        push!(buffer_manager.active_buffers, buffer_id)
        
        return buffer
    end
end

"""
    return_buffer(buffer_manager::IOBufferManager, buffer::Vector{UInt8})

Return buffer to buffer manager for reuse.
"""
function return_buffer(buffer_manager::IOBufferManager, buffer::Vector{UInt8})
    buffer_id = objectid(buffer)
    
    if buffer_id in buffer_manager.active_buffers
        delete!(buffer_manager.active_buffers, buffer_id)
        
        size = length(buffer)
        if !haskey(buffer_manager.buffer_pools, size)
            buffer_manager.buffer_pools[size] = Vector{Vector{UInt8}}()
        end
        
        # Limit pool size to prevent excessive memory usage
        pool = buffer_manager.buffer_pools[size]
        if length(pool) < 10  # Maximum 10 buffers per size
            push!(pool, buffer)
        end
    end
end

"""
    buffer_io_operations(buffer_manager::IOBufferManager, io_func::Function, 
                        data_source, chunk_size::Int)

Perform I/O operations using managed buffers.
"""
function buffer_io_operations(buffer_manager::IOBufferManager, io_func::Function, 
                              data_source, chunk_size::Int)
    buffer = get_buffer(buffer_manager, chunk_size)
    
    try
        result = io_func(data_source, buffer)
        return result
    finally
        return_buffer(buffer_manager, buffer)
    end
end

"""
    manage_temporary_data(func::Function, temp_data_creator::Function)

Manage temporary data with automatic cleanup.
"""
function manage_temporary_data(func::Function, temp_data_creator::Function)
    temp_data = temp_data_creator()
    
    try
        result = func(temp_data)
        return result
    finally
        # Cleanup temporary data
        temp_data = nothing
        GC.gc()
    end
end

"""
    add_reference(counter::ReferenceCounter{T}, key::UInt64, obj::T) where T

Add object reference to reference counter.
"""
function add_reference(counter::ReferenceCounter{T}, key::UInt64, obj::T) where T
    counter.objects[key] = obj
    counter.ref_counts[key] = get(counter.ref_counts, key, 0) + 1
end

"""
    remove_reference(counter::ReferenceCounter{T}, key::UInt64) where T

Remove object reference from reference counter.
"""
function remove_reference(counter::ReferenceCounter{T}, key::UInt64) where T
    if haskey(counter.ref_counts, key)
        counter.ref_counts[key] -= 1
        
        if counter.ref_counts[key] <= 0
            # Object can be cleaned up
            if counter.cleanup_function !== nothing && haskey(counter.objects, key)
                counter.cleanup_function(counter.objects[key])
            end
            
            delete!(counter.objects, key)
            delete!(counter.ref_counts, key)
        end
    end
end

"""
    cleanup_resources(resources::Vector{Any})

Clean up a collection of resources.
"""
function cleanup_resources(resources::Vector{Any})
    for resource in resources
        try
            if applicable(close, resource)
                close(resource)
            elseif applicable(finalize, resource)
                finalize(resource)
            end
        catch e
            @warn "Failed to cleanup resource" resource_type=typeof(resource) exception=e
        end
    end
    
    empty!(resources)
    GC.gc()
end

# Initialize object function - to be implemented based on data types
function initialize_object! end

# Cleanup functions for memory-mapped files
function Base.close(reader::MemoryMappedReader)
    close(reader.file_handle)
    reader.mmap_array = UInt8[]  # Release reference
end

function Base.close(writer::MemoryMappedWriter)
    # Ensure data is flushed
    flush(writer.file_handle)
    close(writer.file_handle)
    writer.mmap_array = UInt8[]  # Release reference
end

end # module MemoryManagement